The present invention relates to a method of analysing ions, a method of mass spectrometry, an analytical instrument for analysing ions and a mass spectrometer.
It is known to perform Data Dependent Acquisitions (“DDA”) using a mass spectrometer wherein an initial survey scan of parent ions is performed. Once an initial survey scan has been performed, parent ions of interest are determined and are then isolated or selected by a quadrupole mass filter. The parent ions of interest are isolated or selected by arranging for the mass filter to transmit just the specific parent ions of interest on the basis of the mass to charge ratio of the parent ions. The parent ions of interest may then be fragmented and resulting fragment ions may then be mass analysed. Mass analysis of the resulting fragment ions enables the parent ions of interest to be identified or the identity of the parent ions of interest to be confirmed.
FIG. 1 shows a known arrangement comprising a quadrupole-Time of Flight mass spectrometer which may be used to perform conventional DDA experiments. Ions from an ion source 1 are transmitted to a quadrupole rod set mass filter 2. A gas collision or fragmentation cell 3 is located downstream of the quadrupole mass filter 2 and an orthogonal acceleration Time of Flight mass analyser 4 is located downstream of the gas collision or fragmentation cell 3.
An initial survey scan may be performed wherein the quadrupole 2 is operated in an ion guiding only mode of operation so that a wide range of precursor or parent ions are onwardly transmitted by the quadrupole 2 to the gas cell 3. The gas cell 3 is also operated in an ion guide only mode of operation (i.e. in a non-fragmenting mode of operation) so that a wide mass to charge range of parent ions are onwardly transmitted to the orthogonal acceleration Time of Flight mass analyser 4 without causing the parent ions to be fragmented. The precursor or parent ions are then mass analysed by the orthogonal acceleration Time of Flight mass analyser 4.
The mass to charge ratio of parent ions of interest as derived from the initial survey scan is then used to control the subsequent operation of the quadrupole mass filter 2 based upon user defined rules.
The quadrupole mass filter 2 is operated so as to sequentially isolate or select specific precursor or parent ions of interest. The parent ions of interest which are onwardly transmitted by the mass filter 2 are then accelerated into the gas cell 3 so as to cause the precursor or parent ions to fragment. The resulting fragment ions are then onwardly transmitted to the orthogonal acceleration Time of Flight mass analyser 4 for subsequent mass analysis.
Fragment ions may be assigned to or correlated with precursor or parent ions with a level of confidence due to the selectivity of the mass filtering stage.
Whilst this approach has proven useful, it is not without drawbacks.
Firstly, the known approach suffers from the problem of having a relatively low duty cycle since a plurality of species of parent ions will arrive at the quadrupole mass filter 2 at substantially the same time but only a single species of parent ions of interest will be onwardly transmitted by the mass filter 2. The other parent ions of interest will be attenuated by the mass filter 2.
Secondly, the known approach can exhibit insufficient selectivity of the isolation step when processing complex mixtures. The latter problem is known as chimeracy. For example, two different species of parent ions may have substantially the same mass to charge ratio. However, the quadrupole mass filter 2 will transmit both species of parent ion since it is unable to distinguish between the two different species of ions.
The first problem of reduced duty cycle arises as a result of the sequential temporal nature of the mass filtering step in conventional DDA experiments. By way of illustration, if the initial survey scan identifies ten precursor or parent ions of interest which are desired to be selected and onwardly transmitted by the mass filter 2, then the quadrupole mass filter 2 will be arranged to select each of the ten different precursor or parent ions individually and in turn. Whilst a particular precursor or parent ion is being isolated or selected the other nine species of precursor or parent ions (by virtue of the fact that they are present in the quadrupole mass filter 2 at the same time) are lost to the quadrupole mass filter 2. As a result, the precursor or parent ion selection duty cycle is only 10%.
The second problem of insufficient isolation or selectivity arises from the fact that multiple precursor or parent ion species may be onwardly transmitted by the quadrupole mass filter 2 during a single isolation stage. This can be due to the limited mass resolution or mass transmission window of the quadrupole mass filter 2 or it can be due to two or more species of precursor or parent ions having substantially the same mass to charge ratio being present at the same time (i.e. an isobaric interference).
It is desired to provide an improved mass spectrometer and method of mass spectrometry.